More tools

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Below is a list of tools that have previously been developed and published by the Gerstein Lab.

To view tools that have been published and are actively being maintained, please click here.

Unpublished resources may be viewed by clicking here.

Literature associated with lab software and servers may be accessed here.


Tools portals


Tool NameRelease DateDescription

we proposed a number of novel trees based on the occurrence of specific features, either folds or orthologs, throughout the whole genome. We call thesegenomic trees or whole-genome trees.

Tool NameRelease DateDescription


a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information


Tool NameRelease DateDescription

A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes.

Network Tools

Tool NameRelease DateDescription
HUB2001A tool for leveraging the structure of the semantic web to enhance information retrieval for proteomics. This tool helps Proteomics researchers to be able to quickly retrieve relevant information from the web and the biomedical literature.
Yeasthub1997A semantic web-based application which demonstrates how a life sciences data warehouse can be built using a native Resource Description Framework (RDF) data store. This data warehouse allows integration of different types of yeast genome data provided by different resources in different formats including the tabular and RDF formats.

Arrays-Based Tools

Tool NameRelease DateDescription
ProCAT 2006A data analysis approach for protein microarrays. ProCAT corrects for background bias and spatial artifacts, identifies significant signals, filters nonspecific spots, and normalizes the resulting signal to protein abundance. ProCAT provides a powerful and flexible new approach for analyzing many types of protein microarrays.
Tilescope2007An online analysis pipeline for high-density tiling microarray data. Tilescope normalizes signals between channels and across arrays, combines replicate experiments, score each array element, and identifies genomic features. The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis.


Tool NameRelease DateDescription
Local Clustering2001A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.


Tool NameRelease DateDescription
BoCaTFBS2006A boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. This tool is based on a data mining approach combining noisy data from ChIP-chip experiments with known binding site patterns. BoCaTFBS uses boosted cascades of classifiers for optimum efficiency, in which components are alternating decision trees; it exploits interpositional correlations; and it explicitly integrates massive negative information from ChIP-chip experiments.
ExpressYourself2003An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
SPINE2001A laboratory-information management system (LIMS) for the NorthEast Structural Genomics Consortium. The online version is restricted to consortium users, but most of the code is freely available for download.

even more tools

Personal tools